From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Wed Nov 05 2008 - 15:58:58 CST
Hi, there:
Is there an upper limit of atom number that NAMD can handle?
I was running a simulation with first 1000 step minimization and
then dynamics. But NAMD existed after the minimization with error
Application 471018 exit signals: Segmentation fault, Killed
And the error in the output file is:
APINFO_NIDTERM: compute node initiated termination, possible out of
memory condition
Is this a problem of limited compute memory? or, the namd
itself(wrong scripts, et al)? How can I estimate the memory needed for
a given atom number?
BTW, the atom numbers of my system is about 15,000
Thanks a lot.
Bin
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